* using log directory ‘/Users/ripley/R/packages/tests-devel/popEpi.Rcheck’
* using R Under development (unstable) (2025-12-24 r89227)
* using platform: aarch64-apple-darwin25.2.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.2
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘popEpi/DESCRIPTION’ ... OK
* this is package ‘popEpi’ version ‘0.4.13’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘popEpi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘popEpi-Ex.R’ failed
The error most likely occurred in:

> ### Name: survmean
> ### Title: Compute Mean Survival Times Using Extrapolation
> ### Aliases: survmean
> 
> ### ** Examples
> 
> 
> library(Epi)
> ## take 500 subjects randomly for demonstration
> data(sire)
> sire <- sire[sire$dg_date < sire$ex_date, ]
> set.seed(1L)
> sire <- sire[sample(x = nrow(sire), size = 500),]
> 
> ## NOTE: recommended to use factor status variable
> x <- Lexis(entry = list(FUT = 0, AGE = dg_age, CAL = get.yrs(dg_date)),
+            exit = list(CAL = get.yrs(ex_date)),
+            data = sire,
+            exit.status = factor(status, levels = 0:2,
+                                 labels = c("alive", "canD", "othD")),
+            merge = TRUE)
NOTE: entry.status has been set to "alive" for all.
> 
> ## phony variable
> set.seed(1L)
> x$group <- rbinom(nrow(x), 1, 0.5)
> ## age group
> x$agegr <- cut(x$dg_age, c(0,45,60,Inf), right=FALSE)
> 
> ## population hazards data  set
> pm <- data.frame(popEpi::popmort)
> names(pm) <- c("sex", "CAL", "AGE", "haz")
> 
> ## breaks to define observed survival estimation
> BL <- list(FUT = seq(0, 10, 1/12))
> 
> ## crude mean survival
> sm1 <- survmean(Surv(FUT, lex.Xst != "alive") ~ 1,
+                 pophaz = pm, data = x, weights = NULL,
+                 breaks = BL)
Error in set(DT, j = (del_cols), value = NULL) : not a resizable vector
Calls: survmean -> setcolsnull -> set
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [24s/25s]
 [25s/25s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [17s/20s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/popEpi.Rcheck/00check.log’
for details.

       94.45 real        79.67 user         9.21 sys